The Night Brennan Walked Away
by Dukefan1982
Summary: Booth and Brennan have a son, Brennan walks away from life. Does she go back? Read it to find out.
1. Chapter 1 Long Nights

**This is my newest one. It is not complete , only the first chapter is written. I will update as time allows, usually weekends. I don't know how long this one will be.**

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Long nights

Special Agent Seeley Booth sat in the shadowy nursery watching the shadows the nightlight casted on the ceiling, rocking his four month old son, Sam.

"Sammy, I know you miss mommy, but you need to go to sleep for a while, I need sleep."

The baby seemed to relax at the word, 'mommy'. Booth smiled. Sammy had always fallen asleep easily for Brennan until that night. Booth was watching TV and Brennan was getting a two month old Sammy to sleep, he didn't want to sleep and after an hour of Brennan trying she called Booth in for reinforcement, and after a mere 10 minutes of Booth rocking him, Sam was asleep.

Booth knew Brennan doubted her abilities to be a mother from the very second they found out they were going to be parents, but he thought they were getting past that. After Sam was in his crib, Booth found Brennan on the couch chewing her lip; something she did when she was unsure about something.

Booth had tried to reassure Brennan that Sam falling asleep in his arms was in no way a reflection of her parenting skills. Brennan said she was okay, but Booth knew she wasn't, the next night Brennan went to karate and never came back.

Booth knew where she was of course, Brennan was in a one bedroom apartment across town, on leave from the lab and she checked her email every few days. Booth would send pictures once a week and Angela got Sammy form daycare on Fridays for a video chat with his mom.

Booth put Sam on his shoulder and began to pace the nursery, "Sammy, Your mom will be back soon, she just needs time to get her mind around being your mom. You know she loves you, right? She tells you that every Friday, I know because sometimes I hang outside Angela's door to listen and see your mom. I miss her Sam, a lot."

Sam's cries that had been lessening in the last few minutes had now stopped and Booth lowered the baby to his bed, kissing his forehead twice, once for him and once for Brennan. Booth walked across the hall and crawled in to bed on Brennan's side.


	2. Chapter 2 Seeing Sam

**I know this is a little out of character, but part of me thinks that if Brennan were taking care of a baby/child and it were upset and she couldn't comfort the child and Booth could it'd shake her up a lot and make her doubt her abilities to be a parent. When they talk in the next chapter Booth isn't going to be completely understanding, he's going to make sure Brennan knows that this wasn't easy for him. It may be a day or so before it's up.**

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Seeing Sam

It had been a long day and all Booth wanted to do is get Sam through his nighttime routine and relax. Booth tossed the mail on the counter and took a dozing Sam to his room until he woke up from his nap. A half hour later Booth was finishing the dishes when the doorbell rang, he walked to it. "Bones?"

"Booth, I know we need to talk about a lot of stuff, but I was wondering if I could see Sam."

"Of course, he's in his crib." Booth step back letting Brennan enter, she headed for the nursery. A few minutes later Booth found Brennan standing over Sam's crib talking to him, Sam was making noises in reply. Booth smiled and walked over to Brennan."Do you want to hold him?"

Brennan nodded, and Booth reached over the rail and picked up Sam."Hi Bud, let's go see mommy." Booth said a silent prayer that Sam wouldn't start crying as soon as he put him in Brennan's arms, he didn't. After a few minutes Booth took Brennan by the shoulders and guided her to the rocking chair, sitting her down and then he left the room to give two of the most important people in his life some time alone. All though he wasn't in the room Booth knew what was going on with one ear glued to the baby monitor, listening for distress from either Brennan or Sam. Ten minutes later Sam started a low whimper, meaning he was getting hungry, but wasn't starving and to the point of a full blown cry. Booth hurried to the nursery, kneeling beside the rocker he said, "Bones, it's time for Sam to have dinner, and you're welcome to feed him if you want." Brennan's smile told Booth all he needed to know. Booth led the way to the kitchen and watched as Brennan buckled Sam into the highchair, Booth nodded in reassurance when Brennan looked at him over her shoulder. Once Sam was buckled in the highchair, Booth appeared with an 'I love Mommy bib' and a jar of squash. Brennan uncapped the jar, "Booth, this stuff smells disgusting!"

Booth smiled "I know, but Sam loves it, he'll eat it like nothing."

Brennan gave Sam his first spoonful and was surprised when he attacked the burnt orange colored foul smelling concoction with gusto. "You weren't kidding, is he like this with all baby food?"

"Pretty much, he isn't that fond of peas."

Brennan smiled and gave Sam another spoonful, when he was done Booth handed Brennan a washrag to clean Sam off, he protested a little."He doesn't like getting his face washed, but he deals."

Brennan smiled and gently cleaned the last bit of squash from the corner of Sam's mouth."Their Sam, all done. Booth, what's next in his routine?" Brennan asked as she unbuckled Sam and pulled him on to her lap.

"Floor time while I-we eat the pizza I ordered while you were feeding him then bath, story, bottle, and bed all activities you are welcome to participate in if you wish."

Brennan kissed the top of Sam's head and smiled, "I'd like that."

"So would I." Booth smiled and got the door as Brennan settled Sam on the floor.

They ate in silence as Brennan couldn't peal her eyes from Sam and Booth couldn't peal his eyes from Brennan. When they finished Booth asked do you want me to get everything ready so you can bathe him?"

"Yes, you'll stay close won't you?"

"Yes. Sam will probably get you soaked, he likes to splash."

"That's fine." Brennan smiled. 40 minutes later a freshly bathed Sam was sitting in Brennan's lap listening as she read a story; Booth was listening in the doorway with a bottle as she finished the book."Bones, he probably won't finish all of this, he's almost out."

Sam drank a little more than half the bottle and was out like a light. Booth found Brennan slowly rocking Sam an hour later.

"Bones, it's almost ten, are you going to spend the night? You can."

"Really?"

"Yes."

"Thank you Booth."

Booth smiled in acceptance.

"Booth, I know we need to talk about all this, but can we do it tomorrow? I need to get my thoughts together."

"Yes."

"Thanks. Booth, does Sam have to go to daycare tomorrow?"

"No, what do you have in mind?"

"I'd like to say home with him, I may not be that good at it, but I need to try."

Booth knelt in front of the rocker, "You'll be good at it Bones, I'll write out Sammy's morning/afternoon routine, following that should make it easier."

"Thanks."

"You're welcome Bones, are you going to take the bed or the couch?"

"Can we both take the bed?"

"Sure."

Brennan smiled and handed Sammy to Booth, he put him in his crib and both parents placed a kiss on his forehead.


	3. Chapter 3 Breakfast Talks

Spaghetti Talks

The next morning Booth got up a half hour earlier than he needed to, to get things ready for Brennan to spend the day with Sam. Booth wasn't nervous about Brennan staying with him; she'd done it when he was a newborn without problems. Booth just wanted to have everything she might need within easy access so mom and baby weren't stressed out.

The night had gone well they both fell asleep on their sides of the bed, not touching, but around 2 Booth woke up to Sam crying and found Brennan snuggled into him. Booth was finishing up writing out Sam's morning/afternoon routine when Brennan came into the kitchen with Sam in her arms. Booth looked up, Sam looked happier than he'd seen him in a while and Brennan looked happy too. "Good morning Bones, did you sleep well?"

"Good morning Booth, I did sleep well last night."

"I'm glad. Let me take Sam while you go get coffee." Brennan smiled and handed Sam over; as soon as Booth took Sam he started to fuss. Brennan looked at Booth slightly questionably; he smiled slightly at her concern. "It's okay Bones, Sam just wants you to take him back and he need to eat. I'll feed him while you change and eat."

Brennan nodded and kissed Sam's head on the way to the bedroom. Brennan came back just as Booth was telling Sam, "Sammy, I'm glad Mommy is back we need her. We need to talk a lot tonight and what I have to say to her will hurt us both, but I have to say it Sam she has to know. Know this however tonight turns out I am not letting your mom leave you again, I don't care if we have to live in separate apartments for the rest of our lives we'll both be there for you." Sam just opened his mouth for another bite of rice and applesauce.

Brenan stood by the door frame. "Booth, I-"Booth's head snapped up."Bones, we'll talk about it all tonight, just enjoy your day with Sam, okay? I wrote everything out for you, the baby food is in the cabinet to the left of the stove, his bottles are made in the fridge, and extra diapers are in the bottom of his closet along with outfits, one onesies are in the top drawer of the dresser. I put the car seat back in your car just in case you need it."

"Okay, thanks Booth." Brennan smiled at Sam downing his food as fast as Booth could feed it to him.

"You're welcome Bones; I'll bring lunch here about noon."

"That's fine."

Brennan watched as Booth finished feeding Sam then he cleaned him up and handed him to Brennan. "Bye Sammy, be good for mommy." Booth then whispered in Brennan's ear, "you'll be fine, Bones." and kissed her cheek, Brennan nodded and watched Booth go.

She and Sam spent the morning on the floor Brennan was amazed when Sam rolled over, she called Booth and told him, he acted surprised to hear even though Sam had learned to do it two days before. At 11 Brennan took Sam into his room and sat in the rocker while he had a bottle, then she read to him.

Booth cam home later than he planned, the line at the diner took forever. Booth came home to a quiet apartment he was happy that nobody was crying but the silence unnerved him. Booth put the food on the table and went to find Brennan he went to the nursery, what he found there made him grin like a fool; Brennan and Sam were asleep in the rocker.

Booth went to the rocker and picked up Sam, the baby stirred as he was lifted from his mother's lap, Booth patted his back as he placed him in the crib. After Sam was settled Booth turned and picked up Brennan, the first thing he noticed was she was lighter than before Booth shook his head as he put Brennan in bed and pulled up the blankets, his famous spaghetti was on order tonight.

With his two charges in bed Booth went to the kitchen and quietly ate scribbling Brennan a note that her salad was in the fridge before heading back to work.


	4. Chapter 4 Spaghetti Talks

Spaghetti Talks

Booth opened the door to the apartment, he didn't want to have this conversation, but like he told Sam this morning Brennan needed to know how much her leaving hurt him and that he wouldn't allow her to leave Sam again. She could leave him, they could live in separate apartments and only speak to each other when Sam's needs were being to be talked about, but he wouldn't allow her to leave their son. Brennan looked up from the couch, where she sat with Sam in her arms "Hi, Booth."

"Hey Bones, did you enjoy your day?"

"Yes."

"Good I'm going to start diner while you feed Sam, then after we eat I'll give him a bath and then you can finish the rest of the night."

"Okay. What will it be tonight, Sam? Carrots?" the baby just looked at Brennan as she carried him into the kitchen. The dinner went smoothly, gentle conversation about their days.

Booth took Sam to give him a bath and when he was getting Sam into his PJ's he knew Brennan was in the doorway and Sam could see her because he wouldn't hold still so Booth could do the snaps up."Hang on Buddy, we'll go se mommy in a minute." Sam let out a squeal; Booth laughed "I see Aunt Angela has rubbed off on you, little man."

Booth finished snapping the snaps and turned handing Sam to Brennan before leaving the room. A half hour later Brennan cam to sit down next to Booth. "Sammy go down okay?"

"Yes, _Goodnight Moon_ and a bottle and he was out like a light." Brennan smiled.

"Good. Bones, we need to talk-."

"I Know. I'm sorry that I left, that night, I had been feeling insecure about being Sam's mother for days, and I didn't know what I was really feeling or what to do about it. When Sam wouldn't go to sleep for me and you got him to sleep I thought I was okay with it, I knew it wasn't my fault.

The next night when you were holding him when I left for karate he looked so happy that when I got in the car something snapped I freaked. I wasn't going to go away for two months it started out as a day at the most, just to get my thoughts together then it snowballed into two months."

Booth got up, walked to the other side of the room, and looked at Brennan."YOU FREAKED What about ME? I fell asleep on the couch only to wake up two hours later to a crying baby and discover that my girlfriend and my Son's mother wasn't home, Bones that scared the living daylights out of me.I thought something happened to you or…or… You didn't answer phone, if you had answered and told me that you needed a night to yourself, I'd let you take it, I'd let you have a night to yourself every week if you needed it. I understand about you being insecure about being a parent, every parent feels that way at some point, but you should have talked to me or Angela or someone." Booth voice got louder with every word.

"Booth, lower your voice you'll wake Sam." Booth cringed.

"Why, so you could tell me that it was normal to feel that way, and it'd be okay? I didn't want that, I wanted to scream and cry and work it out on my own."

"Bones, I get it, but you can't just run when things get hard, believe it or not even though we're not married we are a family. We're in this together, you me and Sam." Brennan didn't look at Booth when she spoke.

"I know Booth, I wanted to answer my phone but I couldn't, I couldn't admit that I couldn't do it, what mother admits they can't handle a baby? I didn't want you to think less of me when I admitted it." To Brennan's credit she didn't cry and to Booth's he resisted the urge to comfort her.

"Temperance, do you honestly think I'd think less of you because you admitted you couldn't do something?" Brennan didn't reply, Booth continued, "If anything I think less of you know because you ran away from Sam, you took the easy out Bones. I have to tell you Bones I don't know where we are now, I'm letting you see Sam because you need to be in his life, but I don't know about us. What if Sam gets too much for you to handle are you going to run again Bones? Because I am NOT letting you leave Sam again, you can leave me, and we can live in separate apartments and only speak to each other when Sam's needs were being to be talked about, but I'm not allowing you to leave our son, he needs his mother."

Brennan sat there "Booth, I didn't take the 'easy out' leaving Sam and you was the hardest thing I've ever done, I didn't want to do it, but I didn't know what else to do. I know I messed this up as much as anyone could but, I'd like another chance. I wanted to come back I drove here a lot of times and sat in the car and willed myself to get out of it, but I couldn't do it. "

"Why couldn't you get out of the car walk to the elevator hit the button for the third floor wait the minute and a half or whatever it is, walk 20 feet use your key and come in here and talk to me?"

"I don't know."

"You don't know? Come on Bones, you can do better than that!"

Brennan willed the tears away."What do you want me to do, Booth? Beg for forgiveness, go away? What?"

"I want a good reason why you couldn't come back to us."

"Booth I don't know what to say other than I was scared to come back, I didn't want to face it."

"Why after two months did you come back now?"

"I did a lot of thinking and I did a lot of reading I am better prepared now. I know I had 9 months to get prepared, but it was different once Sam got here, once I held him it all changed, I lost all rationale."

Booth smiled, "how do I know you're not going to run again, Bones?"

"Booth, you have my word that I am not going to run from Sam or you again, can you trust me?"

"Bones, you're going to have to gain my trust, but this is a start. You're welcome to stay here as long as you want, we can do what we did today. "

"Thanks Booth."

"You're welcome Bones. I'm going to bed, are you coming?"

"In a few minutes, I'm going to check on Sam."

"Okay."

Booth walked past the couch, Brennan reached out to hold his hand, and Booth touched her finger tips as he walked by.

Brennan went to the nursery, Sam was on his side sound asleep, and Brennan fixed the blanket and kissed the baby's forehead. "Sam I'm sorry that I left, I got overwhelmed and instead of talking to your Dad I internalized everything and ran." Brennan couldn't hold the tears in anymore, she stood at the side of the crib and let them go.

She felt two strong arms around her pulling her back."Sam forgives you Bones." Brennan looked up at Booth "Do you?"

"I'm working on it; it's going to take time on both our parts. Let's go to bed, that way you can cry and not worry about waking Sam."

"Okay."

Brennan let Booth take her to their room.


	5. Chapter 5 Taking the Day Off

Taking the Day Off

Booth woke a little earlier than he needed to and wasn't that surprised to see that Brennan was curled into him, he took a moment to enjoy the feeling and ran a hand down her back, Brennan stirred. "Hi."

"Morning Bones."

"Morning Booth. Booth it's Friday, I don't want Sam to go to daycare, but I don't want Angela to know about this. I'm not ready to have that conversation. "

"You don't have to; I told Cullen I'd be taking today off."

"Why, don't you trust me?"

"I do, but I don't. You left us. How do I know you're not going to leave Sammy here…alone?"

"Booth, I'd never leave Sam alone, I left because you were here."

"I know but part off me has doubts, besides I want to spend some time with Sammy and you."

Brennan reply was cut off by a cry. "I'll get him while you call Angela and make the coffee." Booth nodded.

Brennan got Sam ready for the day and fed him. After everyone had eaten Booth and Brennan played and spent time with Sammy until he went down for a nap. Booth sat down next to Brennan."Bones, how did you get past having the conversation with Angela?"

"I told her forcefully I didn't want to talk about it, she tried to get me to tell her but I clammed up."

Why did you send me an email letting me know you were at the double tree?"

"I guess I didn't want to close myself off completely this time. Why didn't you come get me?"

"Because I didn't want to force you into something you weren't ready for or didn't want to do. and I had an unhappy Sammy to deal with he cried the first night we were on our own and every night for the first week and a half after that he was up every 2 hours. Wednesday night was the first time he slept longer than two hours in months."

Brennan sat there, the realization that she'd hurt Sam was too much she got up and ran to their bedroom, shutting the door behind her. Booth waited ten minutes then he went after Brennan.

Booth knocked lightly "Bones?"

"Go away Booth."

Booth opened the door and leaned on the doorframe watching Brennan try to hide the tears and gain control. Booth crossed the room and pulled Brennan to him. "I didn't mean to hurt you or Sam."

"I know you didn't, but you did."

"I'm sorry, Booth."

"I know I'll be able to put it behind me, but it's going to take time."

"I know, I just wish I could do something,"

"You are everyday you spend with Sam and I working though problems and insecurities that you have with this new phase of your life, helps me trust you more. Once we get more into a routine we need to start talking things out, no more internalizing everything and running, okay?"

"Okay."

"Good. I'm going to heat up some leftover spaghetti and when Sammy wakes up we can all head to the park for a bit, it's too nice of a day to be in the apartment all day."

"Okay, that sounds fun. Can you give me a minute to clean up? Then I'll come and have lunch."

"Sure." Booth gave Brennan a hug and went to the kitchen.

An hour and a half later the family was strolling in the park, Booth was pushing the stroller and Brennan had an arm around Booth's waist, they stayed at the park for most of the afternoon. On the way home Brennan turned to Booth,"Booth do you have Parker this weekend."

"Yes."

"Does he-?"

"He asked where you were, I said you went away for a while, Parker assumed you were on a dig, I didn't correct him."

Brennan nodded in acceptance. "Booth, do we have time to stop at the store? I'd like to make the meal I always do when I've been away for an extended period of time and we have Parker, I see no reason to tell him any different."

Booth nodded "Sure. We need diapers and stuff anyway."

The three finished shopping and made it home seconds before Rebecca dropped off Parker. Booth didn't tell Parker Brennan was home, he just let him walk into the kitchen and find her putting the macaroni in the oven.

"Bones! I'm glad you're home, I missed you so much."

Brennan unwound Parker's arms from her waist and picked him up."

"I missed you too Sweetheart, very much."Brennan held onto parker a bit longer and sat him down," go play with your Dad while I finish dinner."

"Okay."

Brennan watched him go and turned her attention to the brownies that were almost done. After a dinner Brennan took Sammy though his night time routine and once he was down she joined Parker and Booth for a movie. By the end of the movie Parker was snuggled in Brennan's lap his head on her chest sleeping soundly. Booth looked over; Brennan was running a hand absently through his hair."Bones let me get him in bed."

Brennan looked down at the sleeping boy in her lap, "no, I'll do it; I need to check on Sam."

"Okay."

Brennan eased up and carried Parker to his room tucking him in and going down the hall to Sam's room, seeing that the baby was sleeping soundly, she smiled and went to Booth.

"Everybody's asleep."

"That's good. Bones you did great with Sammy, he hates to go grocery shopping, Angela watches him on Saturday afternoons so I can go without a screaming baby."

"Thanks Booth, it's the cart Sam doesn't like, he does better if you hold him."

Booth smiled and placed an innocent kiss on Brennan cheek before leading her to their room.


	6. Chapter 6 The Conversation with Angela

The Conversation with Angela

It was a little before 9 am and Brennan was typing away on her laptop she hadn't written anything for months, Booth, Parker and Sam were still asleep. The knock at the door brought Brennan out of her concentration, getting up and looking through the peephole Brennan gowned and opened the door."Angela what are you doing here?"

"Bren, I'm here to watch Sam while Booth takes Parker to soccer practice and grocery shops after. Why are you here?"

"I'll explain in a bit, but first I need to wake up Booth and Parker. What time is soccer?"

"10:15." Brennan nodded and hurried to wake Booth. She stepped into the bedroom, she kissed Booth. "Booth wake up, Parker has soccer practice. "

Booth's eyes flew open," What time is it?"

"A little after 9. Angela's here."

"Sorry Bones I forgot to tell her not to come today."

"Its fine, I need to talk to her today's a good of a time as any. I'll get Parker up and make you two some bagels." Brennan turned and was gone. Booth got up and changed meeting a sleepy Parker in the kitchen."Morning Bob, grab your bagel and let's vamoose."

"Okay Dad."

Booth kissed Brennan's cheek and headed out the door as soon as the door closed, Brennan turned to Angela."Angel, I need to explain. Coffee?"

"Sure."

Brennan got two cups of coffee and sat on the couch, handing one to Angela."I came back Wednesday night, just wanting to see Sam, I did and Booth invited me to stay. We talked, we're working it out it's going to take a while."

"Why did you leave?

"I had been feeling insecure about being Sam's mother for days, and I didn't know what I was really feeling or what to do about it. When Sam wouldn't go to sleep for me and Booth got him to sleep I thought I was okay with it, I knew it wasn't my fault. The next night when Booth was holding him when I left for karate he looked so happy that when I got in the car something snapped I freaked. I wasn't going to go away for two months it started out as a day at the most, just to get my thoughts together then it snowballed into two months."

"I get it Bren, but you should have called me, I had a lot of days like that when Gabby was born."

"You did? What did you do?"

"I spent a lot of nights in the bedroom crying while Jack took care of Gabby, some nights you couldn't tell who was crying more."

"It got better right?"

"Yes, I still have insecure moments, but it's a lot better. Why didn't come back before now, Bren?"

"I did a lot of thinking and I did a lot of reading I am better prepared now. I know I had 9 months to get prepared, but it was different once Sam got here, once I held him it all changed, I lost all rationale. It was like I didn't know what to do"

"Okay but you can't learn it all from books; you just have to do it."

"I know. Why did you do the video chats, Ange?"

"I did them for Sam, he missed you."

Brennan's reply was cut off by Sam's cry, she returned with a happy Sam minutes later."Booth told me Sam was up every 2 hours, but that's was his normal thing."

"Did Booth tell you how he finally got him to sleep after being up for 26 hours with only 30 minute naps?"

Brennan shook her head.

"He got one of your shirts and put it under the crib sheet, so Sammy was lying on it at all times, every few days he'd either change the shirt or spray a little of your perfume on it so it'd smell like you. Sammy would sleep then, but only if he was on your shirt."

"Why didn't either of you tell me?"

"We didn't want to guilt you into coming back if you didn't want to."

"I wanted to come back but I couldn't face Booth I didn't want him to think less of me when I admitted I couldn't handle Sam what mother admits they can't handle a baby?"

"A sane one. Sweetie Booth wouldn't think less of you if you admitted you had misgivings about being a parent, he would have helped you through it."

"I know that now. But Booth does think less of me now."

"Can you blame him? You walked out on your son."

"No, I'd have done the same if I were in his position. I just wish he wasn't as mad at me as he is, he has every right to be of course, but it's killing me."

"Sweetie all Booth needs is time."

"I know." The two friends chatted a while longer, then Angela left Brennan and Sam on the couch reading a book. Twenty minutes later Booth opened the door carrying Parker, he sat the boy on the couch before explaining."Parker fell and sprained his ankle." Brennan handed Sam to Booth, turning her attention to Parker."Parker, I need to look at your ankle."

"No, you'll make it hurt worse."

"Parker, I know it hurts but I need to look and make sure that spraining it is all you did. I'll go slowly and if it hurts too much I'll stop, okay?"

"K."

Brennan gently took off Parker's shoe and sock, her fingers going over Parkers slightly swollen ankle, he winced."I'm almost done Bub, can you hold on a bit longer?" Parker nodded.

Brennan smiled and finished her exam and put her arm around Parker's shoulders.

"It's a mild sprain, nothing rest elevation, ice, and a mild anti-inflammatory can't fix."Brennan kissed the top of Parker's head and went to get an ice pack. Brennan waked back to the couch and propped Parker's leg up on pillows and gently placed the ice on his ankle. Booth came with medicine. A half an hour or so later booth went to check the ice it was melted and parker was asleep, so Booth took it and covered him up. An hour later Parker woke up."Park how's the ankle?"

"It still hurts."

"Do you want more ice?"

"Yeah, but can Bones put it on? It doesn't hurt if she does it."

Booth smiled "Sure. Let me go get her."

Parker nodded. Booth went to the bedroom."Bones, Parker's awake, he wants more ice, but he wants you to put it on his ankle."

Brennan looked up from her laptop."Why? I thought he'd want his dad to take care of him."

"Bones, he's hurt and doesn't feel well, he wants his Mom."

"But I'm not-"

"Yes you are, maybe not biologically, but for all intents and purposes you are. Let's switch kids, you take Park, I'll take Sam."

"Okay." Brennan saved her work and went to get more ice for Parker; she gently picked him up and settled him in her lap, putting the ice on Parker's ankle. After Parker was set with the ice Brennan picked up the book Booth had started reading to Parker a few weeks before and began reading aloud, after a while Booth and Sam joined her on the other end of the couch. For the rest of the day Brennan took care of Parker while Booth took care of Sam.


	7. Chapter 7 Moving On

**A/N This chapter is a long time in coming I know, sorry. I have a month of classes left and a thousand things to do! I'll put up a chapter next weekend. **

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Moving on

Brennan had been home for a month, it was going great she and Booth had talks about anything and everything after Sammy was down for the night. They talked about their days and anything else that had been bothering them. Brennan felt better in the last month than she had all year and she knew having Booth to talk to and knowing whatever she said he'd take in stride and help her thought was the reason. Booth felt better too, his Bones was back and together they were working through her issues. Booth went back to work two weeks after Brennan came back, he hadn't wanted to, but he needed to show Brennan that he trusted her enough to be with Sammy on her own. He had lunch with her every day, more often than not he'd find them in the rocking chair reading and sometimes they'd both be asleep on those days he'd put everyone in their beds and stick Brennan's salad in the fridge.

It was a Friday night and Booth was making bowtie pasta and steamed vegetables while Brennan fed Sam, they took turns with everything except putting Sam to bed at night that was Brennan's thing. Booth knew something was bothering Brennan, she'd been quiet and distant at lunch. Booth knew he had to get Brennan to talk about it, but he decided to wait until Sammy was in bed, Brennan seemed to be more willing to open up once he was in bed. They had dinner spent a little time with Sammy, and then Brennan took him and got him ready for the night an hour later Brennan sat down next to Booth."Sammy go down okay?"

"Yes, I didn't read to him tonight, he didn't have a good nap this afternoon he was out almost as soon as I gave him the bottle."

"That's good."Booth sat a moment, "Bones what's wrong?"

"Nothing, you'll think it's stupid."

"Whatever it is I won't, you can tell me."Booth squeezed her hand.

Brennan took a breath, "My rent is due on Monday and I don't know if I should pay it or stay here."

Booth brought Brennan's face up,"Bones, you can stay here if you want to or we can live in separate apartments, it's up to you."

"I want to live here, but I don't-"

"You don't what Bones?"

"I don't know if you want me here Booth."

"I want you here Bones. What do you say we go get your stuff tomorrow and go to the diner for lunch?"

"What about Sam?"

"Angela can watch him."

"Okay."Booth could tell something was still bothering Brennan, he cupped her cheek. "Out with it Bones."

She took another breath" karate starts back Monday night, I haven't gone since that night, and I'd like to go."

"Then go bones I'm not going to tell you, you can or can't go."

"But last time-"

"Stop Bones! Let me ask you something, do you feel like you did the night you left? Or even a few days before?"

"No, I feel better now than I have in months."

Booth smiled, "Go Bones I'm not worried about you freaking out and leaving again. You're doing well handling Sam and the challenges he brings to the both of us, you don't hold things back anymore if something is bothering you, you've come a long way."

"Really?"

"Yes, it still is in the back of my mind, but I don't leave the apartment every morning worried about what I'll find when come home anymore. I think it's time we start putting it behind us and move on, I am still working on trusting you, but it's a lot better than it was; I see no reason to dwell on it anymore."

Booth gently kissed Brennan.

"Thank you, Booth."

The next morning Brennan packed Sam up and took him to Angela's then she and Booth packed up her meager belongings in the furnished apartment, all Brennan had was a few clothes, books and some photos of Sam. Sunday was a lazy day. Monday night Brennan fed Sam and bathed him while Booth got dinner ready then after dinner Brennan grabbed her gym bag and left, kissing a drowsy Sam and a contented Booth on the way out. Two hours later Brennan unlocked the door to a quiet apartment and a sleeping Booth on the couch, smiling Brennan clicked off the TV and dropped a blanket over Booth. Brennan leaned down to kiss Booth's forehead, his hand came up pulling her down to him.

"Booth I'm tired and would like to go to sleep."

"So go, I'm not stopping you."

"I can't the couch isn't big enough and we haven't been this close for a long time."

"I know, but like I said, I think it's time we start putting things behind us and move on. We don't have to go all the way, but I think sleeping with less than a foot of space between us is a start."

"Brennan didn't reply she just snuggled down and after a few minutes Booth sat up and carried Brennan to bed.


	8. Chapter 8 Holding Back

Holding Back

Brennan had been home with Sam for two months she didn't want to leave him, but she wanted to go back to work."Sam, what do you think about overalls and a striped shirt?" Brennan grabbed the items from the closet and took them and Sam over to the changing table and began to dress him."Sam, I don't want to leave you, but I want to go back to work, not that I haven't enjoyed our time together I have." Sam responded by grabbing for Brennan's necklace as she sat him up to pull the shirt over his head, she blocked his hand."I don't think so mister."Brennan ticked Sam's tummy, making him giggle."I wish I could take you with me; I don't like it when we're apart but you Dad would have a fit if you spent your days at the lab. He's right though, you wouldn't receive adequate stimulation while we were working, but hopefully you'll come for a visit now and then. There all done." Sam gave Brennan a drool-y smile as she picked him up.

Shortly after Sam was ready they took him to daycare, it wasn't as easy as it had been for two reasons, one Sammy was now more alert and knew what was going on and two he'd grown really attached to Brennan and didn't want her to leave. Booth wrapped an arm around Brennan's waist. "You okay, Bones?"

Brennan smiled a little" I will be its harder now." Booth kissed Brennan's cheek. "I know, I wish it wasn't."

The week passed okay, no cases meant Brennan was in limbo and Booth was dragging her home by 4.

Booth wasn't looking forward to Thursday; it was their fist therapy session with Sweets.

"You ready to go Bones?"

Brennan looked up from the femur she was squinting at,"Do we have to?"

Booth laughed Brennan's tone was the same one Parker used at bedtime.

"Yes, we'll go torture the kid for a while pick up our own and then go home and have dinner, it won't be so bad."

"Fine."

"Agent Booth, Doctor Brennan it's nice to see you again."

"You too Sweets." The partners took up residence on the couch.

"Dr. Brennan, Agent Booth tells me your back after dealing with some issues you had regarding your ability to be a parent to Sam, correct?"

"Yes, Booth and I are working things out on our own and it is going well."

"That's great, but if either of you have something to say to one another and don't know how to say it or need to talk about something you're not sure that you want the other to know, I'll be glad to help."

Both partners nodded, Sweets noticed that Brennan looked like she wanted to say something, "Dr. Brennan do you want to say something?"

"Y-Yes."

"Okay, continue."

Brennan turned in her seat to face Booth."Booth, every time we talk about how hard my leaving was I get the feeling you aren't telling me everything."

Booth looked at Sweets the psychologist nodded," Bones, when you left it felt like someone ripped my heart out of my chest, squeezed it the stomped on it for good measure. I didn't know what to do, I was mad; I hurt more than I ever thought I could. I hated you, I never thought I could hate you, but apparently I can. I was in a daze for a week, I didn't go to work, and I just sat on the couch and took care of Sam. Then when Sam got calmed down I had Angela watch him and I went to the range and fired till I ran out of bullets then I went to some hole in the wall bar and got very drunk. I even willingly talked to Sweets Bones, I didn't want to, but I knew I had to do something."

Brennan stiffened willing the tears away, "Do you hate me still?"

"No, for a while when you first came back I did, but now I'm getting over it."

"I'm sorry Booth, I didn't-"

"I know Bones." Booth softly kissed her, sweets cleared his throat, the partners looked at him."You've got about a half hour left, go get Sam and go home have dinner and talk it out, you both are doing good you don't really need me for this. Just remember that no matter how bad this gets and however bad it hurts you need to let it all out."

"Thanks Sweets." The psychologist nodded, picking up his notebook and writing a note. Booth waited in the SUV while Brennan got Sam from daycare. Booth ordered the Thai while Brennan fed Sam. When he was down for the night Booth and Brennan talked it out, they both were drained in the end, but they felt good.

**A/N there will be another wait for the next chapter, sorry my sister is coming Friday and staying until Thursday no fic writing time for me.**


	9. Chapter 9 Staying Home

**A/N It's a bird, it's a plane, it's a new chapter! Yes, I know this is very late, but muse has been on other things. I hope everyone likes this one. Only one more chapter, I hope to have it up this week I want to have this one done before summer school starts next Tuesday, I won't have much time when it starts.**

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Staying Home

Sam was a year old and Brennan found it easier to take care of him as he got older. Brennan was more at ease now; she didn't panic over the little things as much now. The last two days had been the test, Booth was at a conference and Brennan was home with Sam, she hadn't called Booth panicking. She had called to tell him goodnight and once because she said Sammy missed him, but other than the goodnight phone calls things were good. Booth just couldn't wait to see the two of them, over the year he and Brennan seemed to get closer after they began moving on. Booth unlocked the door and smiled when Sammy totted over and grabbed his legs; Booth bent and lifted Sammy over his head, making the baby giggle."Hi-ya little man! Did you miss me?" Sammy rested his head on Booth's shoulder in reply."I missed you too bud. Let's go find mommy." Booth found Brennan in the kitchen taking the macaroni and cheese from the oven.

"Hi Bones."

Brennan smiled, "Hello Booth perfect timing, it's done. Can you and Sammy take the salad to the table?"

"Sure." Booth shifted Sammy in his arms and picked up the bowl once the salad was on the table, Booth situated Sammy in his highchair. Brennan carried dinner to the table and put a little macaroni on a small plate and let it cool before giving Sammy the plate and a small spoon. Everyone ate for a minute then Booth asked,"Bones, how was the lab today?"

"I don't know I didn't go."

Booth's forkful of macaroni stopped halfway to his mouth."What? Why?"

"Sammy was really clingy when he woke up this morning and we cleared the case before you left so, I stayed home."

Booth smiled, "Sammy okay?"

"Yes, he's had a very slight fever this afternoon, but I think he's just getting a tooth, his gums are a little swollen."

Booth tried to hide his groan, Sammy didn't handle teething that well.

"We read a little and he took a nap then he just sat on my lap."

Booth smiled, "Bones, I'm proud of you."

"You are, why?"

"The old Bones wouldn't have dropped everything to stay home with a teething one year old, reading to and holding him."

"Thanks Booth."

"You're welcome Bones."

"Booth, you can do all of Sammy's nighttime routine if you want."

"Really? You usually put him to bed; it's the highlight of your day."

"It is and I enjoy it, but you haven't seen him for two days, you need you spend time with him."

"Thanks Bones."

"You're welcome, Booth."

The family finished dinner and Booth gave Sammy his bath, read him a story and put him to bed. Booth found Brennan typing on her laptop."Sammy go down okay?"

"He went down, but he won't be down for long. Poor baby, he's already started getting fussy."

Brennan frowned, she hated when Sammy got like this and there wasn't really much she could do to comfort him."Go to bed Booth I'll get up with Sammy."

"You sure Bones?"

"Yes, you've been at a conference for two days and we both know you don't sleep well away from home."

Booth kissed Brennan, "thanks Bones."

Brennan smiled and went back to her book, thirty minutes later Sammy was up and all Brennan could do was rock him hoping that would soothe him.


	10. Chapter 10 Tummy Ache

Tummy Ache

Sammy was two and half; things had changed a lot in Doctor Temperance Brennan's life, all for the better. The biggest changes were he and Booth had gotten married six months ago and bought a house and were think of adding to the family soon. Brennan was so engrossed in her work she didn't hear the lab doors open; she looked up when she heard Booth call her name. "Bones."

Booth stood at the bottom of the stairs with Sammy, Brennan knew something was wrong; Sammy was letting Booth carry him and not straining to get down and run up the stairs to her, and he was pale. Brennan shed her gloves and grabbed a squirt of the antibacterial foam she kept everywhere in the lab and went down the stairs. Booth handed Sam to her before speaking.' Shannon called; he's got a fever, they can't keep him at daycare."

Brennan nodded and looked at Sam, "Sweetie does your tummy hurt? "

Sammy nodded."Okay we'll go home. Booth, take us home, please."

Booth nodded and put his hand on the small of Brennan's back leading her to her office. Brennan took two steps when she remembered they had a case."Cam-"

Cam smiled, "Go Brennan takes whatever time you need. Wendell and I can handle things."

"Thanks."

"You're welcome, feel better Sammy."

Booth packed Brennan's stuff while she held Sammy. They got home and Brennan took a sleeping Sammy in house, Booth stayed long enough for Brennan to change clothes.

"Do you want me to stay?"

"No, I hope it's not the stomach flu, it's going around and Ange and Gabby had it last week."

Booth groaned, "Do you want me to bring dinner?"

"Yeah, the usual plus some soup for Sammy."

"Okay."

Four hours later Booth came home to Brennan holding Sammy a plastic tub next to him.

"When did it start?"

"About an hour ago, he waned some water, it stayed down less than a minute. He doesn't give you much warning so the tub is easier."

"Mommy." Brennan put the tub in Sammy's lap and waited, rubbing his back. When Sammy was done Brennan cleaned him up and went to the bathroom. Sammy saw Booth and reached for him, Booth picked him up and sat down."Daddy, I don't feel good."

"I know Bud I'm sorry .you'll feel better soon."

"K. I'm tired."

"Close your eyes and go to sleep, Sammy." Booth rubbed Sammy's back.

Brennan came in then, Booth held a finger to his lips. "He's almost out, go eat and I'll sit here." Brennan kissed Sammy's forehead, "he still has a fever when we got home it was 100.4, it doesn't feel any higher. "

Two hours later Sammy woke up, lying on the couch. "Mommy?"

Brennan sat down on the couch,"How do you feel Sammy?"

The little boy shrugged. Brennan smiled; Sammy looked pitiful lying on the couch."How's your tummy?"

Again the little boy shrugged.

"Sammy, you need to at least drink something."

"No, I'll get sick."

Brennan's heart broke. "Sammy, you need fluids or you're going to get sicker. How about a popsicle?"

Sammy lit up a little and nodded, Booth came with a cherry Popsicle and a paper towel for drips. Sammy sat on Brennan's lap and happily munched his Popsicle and watched Dumbo. The night went smoothly, Sammy was able to keep down the Popsicle and a little ginger ale, his fever had also stated going down. At bedtime Sammy wouldn't go down in less Brennan stayed with him, after she thought Sammy was asleep she went out to talk to Booth she got as far as the couch when "Mommy I need you!" was bellowed though the house. Booth smiled," guess you better go. Want me to bring the spare mattress in?"

"No, he wants me to hold him, luckily he has a twin mattress and if I lie down and put my arms around him, he seems satisfied."

A few hours later Booth went to bed, peaking in Sammy's room on the way he smiled Brennan was holding Sammy close while they both slept. Booth went to bed thinking about how much Brennan had changes since she came back, she was more involved in being a parent she didn't stay at the lab past 5 anymore in less it was absolutely necessary even then Booth and Sammy camped out in her office. She didn't work on the weekends unless it was on her book or again absolutely necessary. She dropped everything anytime Sammy or Parker needed her.

A week later Sammy was fine and back at daycare, Booth approached Brennan's desk.

"Bones?"

"Booth, I don't feel very well, my stomach hurts and I think I have a fever."

"I know Cam called and asked me to come take you home. You probably have what Sammy had."

Brennan nodded and let Booth pack her stuff and take her home.

"Booth, what about the kids?"

"I talked to your dad, he's taking Sammy for the weekend and I switched weekends with Rebecca. Now go get in bed and rest."

"You aren't going back to work?"

"No, I'm going to take care of you."

Brennan smiled,"You'll more than likely get the flu."

"I don't care, you're sick and you shouldn't be left alone in case you get too dehydrated or something."

"Thanks Booth." Brennan drifted off.

The End!

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**A/N thanks everyone for sticking with me, even though the story was OOC and the first few chapters weren't that well received and through the long wait for updates! **


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